Multi-Echo fMRI
Intro
What is multi-echo fMRI? https://tedana.readthedocs.io/en/stable/multi-echo.html
Advantages: can tell motion and non-motion: if slope is non-normal, you can remove it.
Literature
lynch, charles j., jonathan d. power, matthew a. scult, marc dubin, faith m. gunning, and conor liston. “rapid precision functional mapping of individuals using multi-echo fmri.” cell reports 33, no. 12 (2020): 108540. https://doi.org/10.1016/j.celrep.2020.108540 .
lynch, charles j., immanuel elbau, and conor liston. “improving precision functional mapping routines with multi-echo fmri.” current opinion in behavioral sciences 40 (august 1, 2021): 113–19. https://doi.org/10.1016/j.cobeha.2021.03.017 .
Misc Notes
- first echo time as early as possible
- second echo as close to normal fmri echo as possible
Example: te1=12ms (this is the earliest the scanner can do); te2=30ms; te3= 48ms.
GE sequence example
adult -> other
minimum 3 echos
tr = 2,000
multiband aspect isn't super important
nova coil
hypermepi01
| series | type | name | time | notes |
| 3 | 3dt1 | sag fspgr 3d .9x.9x.9 | 4:57 | fov 24, matrix 256x256 |
| 4 | 3dt2 | 4:21 | fov 24, matrix 256x256 | |
| 5 | fmri hyper mepi | 12:20 | 3echo, tr=2000; te=30; fov 28.8; matrix 96; 45 slices, 370 volumes; cvs: image_size=96; pepolar=0 | |
| 6 | fmri hyper mepi | 40s | 3echo, tr=2000; te=30; fov 28.8; matrix 96; 45 slices, 370 volumes; cvs: image_size=96; pepolar=1 | |
| 100/7? | fmri se | 18s | pepolar=0 | |
| 8 | fmri se | 18s | pepolar=1 | |
| 9 | fmri hyper mepi | 7mins | 4echo, tr=2000; te=30; fov 28.8; matrix 96; 45 slices, 200? volumes; cvs: image_size=96; pepolar=0 |
total time = 44 mins
BIDS
Config file creation
t1w=3
fmri1=5
fmap1=6
fmap2=7
innert1=$(jq -n --arg dt anat \
--arg md T1w \
--arg fn "$(printf "%03g" $t1w)*" \
'{datatype:$dt, suffix:$md, criteria:{SidecarFilename:$fn}}'
)
innerfmrie1=$(jq -n --arg dt func \
--arg md bold \
--arg cl task-rest_echo-1 \
--arg fn "$(printf "%03g" $fmri1)*" \
'{datatype:$dt, suffix:$md, custom_entities:$cl, criteria:{SidecarFilename:$fn, EchoNumber:1}, sidecarChanges:{TaskName:"rest"}}'
)
innerfmrie2=$(jq -n --arg dt func \
--arg md bold \
--arg cl task-rest_echo-2 \
--arg fn "$(printf "%03g" $fmri1)*" \
'{datatype:$dt, suffix:$md, custom_entities:$cl, criteria:{SidecarFilename:$fn, EchoNumber:2}, sidecarChanges:{TaskName:"rest"}}'
)
innerfmrie3=$(jq -n --arg dt func \
--arg md bold \
--arg cl task-rest_echo-3 \
--arg fn "$(printf "%03g" $fmri1)*" \
'{datatype:$dt, suffix:$md, custom_entities:$cl, criteria:{SidecarFilename:$fn, EchoNumber:3}, sidecarChanges:{TaskName:"rest"}}'
)
innerfmap1=$(jq -n --arg dt fmap \
--arg md epi \
--arg cl dir-PA \
--arg fn "$(printf "%03g" $fmap1)*" \
'{datatype:$dt, suffix:$md, custom_entities:$cl, criteria:{SidecarFilename:$fn}, sidecarChanges:{IntendedFor:["rest-echo1","rest-echo2","rest-echo3"], B0FieldIdentifier:"pepolar_fmap0"}}'
)
innerfmap2=$(jq -n --arg dt fmap \
--arg md epi \
--arg cl dir-AP \
--arg fn "$(printf "%03g" $fmap2)*" \
'{datatype:$dt, suffix:$md, custom_entities:$cl, criteria:{SidecarFilename:$fn}, sidecarChanges:{IntendedFor:["rest-echo1","rest-echo2","rest-echo3"], B0FieldIdentifier:"pepolar_fmap0"}}'
jq -n --arg dcm2niixOptions "-b y -ba y -z y -f '%3s_%f_%d_%r'" \
--argjson descriptions "[$innert1, $innerfmrie1, $innerfmrie2, $innerfmrie3, $innerfmap1, $innerfmap2]" \
'$ARGS.named' > BIDS_config.jsonCreates:
{
"dcm2niixOptions": "-b y -ba y -z y -f '%3s_%f_%d_%r'",
"descriptions": [
{
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SidecarFilename": "003*"
}
},
{
"id": "rest-echo1"
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest_echo-1",
"criteria": {
"SidecarFilename": "005*",
"EchoNumber": 1
},
"sidecarChanges": {
"TaskName": "rest"
}
},
{
"id": "rest-echo2"
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest_echo-2",
"criteria": {
"SidecarFilename": "005*",
"EchoNumber": 2
},
"sidecarChanges": {
"TaskName": "rest"
}
},
{
"id": "rest-echo3"
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest_echo-3",
"criteria": {
"SidecarFilename": "005*",
"EchoNumber": 3
},
"sidecarChanges": {
"TaskName": "rest"
}
},
{
"datatype": "fmap",
"suffix": "epi",
"custom_entities": "dir-PA",
"criteria": {
"SidecarFilename": "006*"
},
"sidecar_changes": {
"IntendedFor": [
"rest-echo1",
"rest-echo2",
"rest-echo3"
],
"B0FieldIdentifier": "pepolar_fmap0"
}
},
{
"datatype": "fmap",
"suffix": "epi",
"custom_entities": "dir-AP",
"criteria": {
"SidecarFilename": "007*"
"sidecar_changes": {
"IntendedFor": [
"rest-echo1",
"rest-echo2",
"rest-echo3"
],
"B0FieldIdentifier": "pepolar_fmap0"
}
}
]
}note EchoNumber and CustomLabels for func
dcm2bids -d sourcedata/${subid}/bids/ -p ${subid} -c sourcedata/${subid}/bids/BIDS_config.json -o . --forceDcm2niixYou then have to delete the bval and bvec files (not sure why they are made) from the resulting func folders:
rm sub-${subid}/func/*.bv*bids-validator should then run without any major errors
Fastsurfer
see fastsurfer for information about Fastsurfer
requires ~4Gb of GPU
Example:
docker run --gpus all -v /mnt/WeberLab/Projects/HYPER-MEPI/sub-${subid}/anat:/data -v /mnt/WeberLab/Projects/HYPER-MEPI/derivatives/FastSurfer:/output -v /home/aweber:/fs_license --rm fastsurfer:gpu --fs
_license /fs_license/license.txt --t1 /data/sub-${subid}_T1w.nii.gz --sid sub-${subid} --sd /output --parallelTakes ~43 mins
fMRIprep
see fmriprep for information about fmriprep
Example:
fmriprep-docker $PWD $PWD/derivatives/fmriprep participant --participant-label ${subid} --fs-license-file /home/aweber/license.txt --dummy-scans 10 --use-aroma --me-output-echos -w /home/aweber/fmriprep_work --fs-subjects-dir $PWD/derivatives/FastSurferTook about 1.5 hours
Then run tedana